Table 1

Differential expression data based on array experiments and Q-PCR of endomesoderm marker genes

EM markers

Expression

Regulation

P value

Q-PCR ratio ± error


Brachyury

537REA_5B8

EM

Li 1.69

Zn 0.42

1.08 × e-06

3.89 × e-03

1.64 ± 0.21

0.33 ± 0.10

Blimp1

537REA_16B13

E

Li 1.33

Zn 0.42

3.98 × e-02

2.58 × e-03

1.78 ± 0.09

0.53 ± 0.04

CoA-reductase

536REAsu2_4L15

EM

Li 0.40

Zn 1.31

5.68 × e-08

1.20 × e-03

0.44 ± 0.03

1.71 ± 0.50

Delta

536REAsu4_17C2

SMC

Li 1.79

Zn NA

1.64 × e-01

NA

4.86 ± 1.05

0.95 ± 0.14

Dlx

537REA_9O11

EM-Oect

Li 0.09

Zn NA

2.60 × e-05

NA

0.03 ± 0.00

0.58 ± 0.26

Endo16

536REAsu2_5N1

E

Li 1.20

Zn 0.46

3.00 × e-01

2.05 × e-04

1.76 ± 0.34

1.70 ± 0.12a

Eve

537REA_2G8

E

Li 1.33

Zn nd

4.89 × e-03

nd

0.93 ± 0.01a

1.73 ± 0.10

FoxA

537REA_10P13

EM+Oect

Li 1.37

Zn na

1.37 × e-06

na

3.18 ± 0.12

1.69 ± 0.43

GataE

537REA_3C9

E

Li 1.55

Zn 0.48

2.77 × e-03

1.71 × e-03

3.06 ± 0.92

0.23 ± 0.04

Hex

SpSMBLAS_124N22

M

Li 1.54

Zn nd

3.99 × e-01

nd

3.22 ± 0.53

0.33 ± 0.03

Hox11/13b

537REA_12K1

E

Li 1.69

Zn na

3.44 × e-09

na

na

na

KRL

PMC_BG781437

EM

Li

Zn

1.90 ± 0.03

5.95 ± 0.66

Lox

536REAsu4_13M18

E

Li ne

Zn 0.36

ne

5.17 × e-03

ne

0.04 ± 0.01

Notch

RUDIREA_30E15

E

Li 1.27

Zn na

4.84 × e-01

na

1.81 ± 0.18

13.5 ± 3.41

P19

537REA_15K13

PMC

Li 1.07

Zn 1.58

7.82 × e-01

3.43 × e-03

1.66 ± 0.33

2.14 ± 0.22

PMAR1

PMC

Li na

Zn na

na

na

1.77 ± 0.29

0.50 ± 0.02

Prox

RUDIREA_15N17

M

Li 0.57

Zn na

2.40 × e-04

na

0.81 ± 0.16

1.46 ± 0.27

Six3

RUDIREA_40B23

Apical, later +EM

Li 0.72

Zn 0.10

7.83 × e-02

6.46 × e-03

0.39 ± 0.04

1.15 ± 0.15a

SM50

RUDIREA_5L2

PMC

Li 0.57

Zn 1.55

1.09 × e-05

1.20 × e-04

1.07 ± 0.19a

18.12 ± 2.93

SMAD2

RUDIREA_24O7

PMC

Li 0.50

Zn NA

2.49 × e-01

NA

0.52 ± 0.09

1.20 ± 0.32

Snail

RUDIREA_13L18

EM

Li 0.99

Zn 0.26

9.72 × e-01

9.05 × e-05

0.24 ± 0.01

0.09 ± 0.01

Sox4

RUDIREA_2H10

EM, later +apical

Li 1.15

Zn nd

4.23 × e-01

nd

1.67 ± 0.21

1.05 ± 0.08

SuH

621REA_14C17

EM

Li 0.24

Zn NA

3.75 × e-02

NA

4.24 ± 0.95a

4.61 ± 1.50

T-Brain

621Rea_6N24

M

Li 0.82

Zn na

6.93 × e-01

na

1.40 ± 0.31a

2.18 ± 0.12

Tbx6

RUDIREA_29D1

M

Li 0.64

Zn 0.74

6.71 × e-05

1.78 × e-05

0.33 ± 0.15

0.16 ± 0.04

Unknown

536REAsu4_13G12

EM

Li 2.23

Zn 4.05

2.69 × e-07

5.52 × e-10

4,68 ± 0.72

11,01 ± 0,27

Wnt3

RUDIREA_28M14

EM

Li 0.89

Zn NA

7.86 × e-01

NA

2.29 ± 0.97a

0.09 ± 0.03

Wnt5

RUDIREA_16P23

EM

Li 1.25

Zn NA

1.97 × e-01

NA

6.31 ± 2.31

1.08 ± 0.08

Wnt8

537REA_10K11

EM

Li 1.35

Zn NA

4.19 × e-03

NA

2.49 ± 0.07

11.36 ± 1.13


The first column gives the gene name and the clone ID, both of which can be used to query the described database [22] for additional data. In the second column the localization of expression in the embryo is given, where EM is endomesoderm, E is endoderm, M is mesoderm, PMC is primary mesenchyme cell, and SMC is secondary mesenchyme cell, Oect is oral ectoderm. The third column (Regulation) gives the differential expression ratios (expression in treatment/expression control) based on the array experiment for lithium (Li) and zinc (Zn) treated embryos (values above 1 indicate upregulation and values below 1 indicate downregulation). The column 'P value' indicates the statistical probability that the regulation could happen by chance (see Materials and methods for detail). The column Q-PCR (quantitative real-time polymerase chain reaction) gives the differential expression ratios (expression in treatment/expression control) and the error, as determined by Q-PCR. (Values expressed in copies of mRNA molecules/embryo are provided via the expressed sequence tag database [75]; see Materials and methods for details on Q-PCR). aDifferential expression based on array and Q-PCR data do not correlate. na, not analyzed; nd, no statistically relevant differential expression; ne, not expressed; ?, expression pattern unknown.

Poustka et al. Genome Biology 2007 8:R85   doi:10.1186/gb-2007-8-5-r85

Open Data